Jmol is a free, open source molecule viewer for students,
educators, and researchers in chemistry, biochemistry, physics, and materials science.
It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

The JSmol JmolApplet is a web browser JavaScript application that can be
integrated easily into web pages. Though Java-based for development and management,
JSmol is completely JavaScript.

The Jmol application is a stand-alone Java application (Jmol.jar)
that runs on the desktop. It has all the capabilities of the JSmol applet but runs approximately 3-6 times faster.
In addition, it can be run in "headless" mode (JmolData.jar) in order to carry out tasks that need to be replicated.

Jmol.jar can be integrated into any other Java program, providing file loading, structure processing, viewing, and output capabilities.

The JmolApplet is a web browser applet that can be
integrated into web pages. It is ideal for development
of web-based courseware and web-accessible
chemical databases. The JmolApplet provides an upgrade path
for users of the Chime plug-in.

The Jmol application is a standalone Java application
that runs on the desktop.

The JmolViewer can be integrated as a component
into other Java applications.

Schematic shapes for secondary structures in biomolecules, including DSSR for investigating the secondary structure of nucleic acids.

Measurements

distance

angle

torsion angle

Support for RasMol/Chime scripting language

Exports to jpg, png, pngj (a png image that can be dragged back into Jmol to reproduce the exact model state the image was created from) gif, ppm, pdf, POV-Ray, Gaussian, Maya, vrml, x3d, idtf, web page.

Those with interest in molecular visualization, especially
the education and research communities, are encouraged
to join the jmol-users mailing list or even the
jmol-developers mailing list.
There you can share ideas and experiences, ask for help,
give us feedback, request new features or changes,
discuss implementation, submit patches, or contribute code.

Without subscribing to any lists, you can also search the archives that collect all messages posted to the lists.